I am experiencing this in a less critical way too, the borders (right from the minimap, between console and textwindow and between text and Sidebar, and the tabs) seems buggy.I experienced this normally only with a huge project and/or sometimes a great workload (opening extra windows in groups etc...)

Most annoying is, that very often the tabs are invisible as long as the cursor is not within the tab-bar.I got this first with SF3 too, and a revert has not solved it. In fact i tried it several times, due too checking if any plugin may cause this behaviour. (It was not, despite they seem to fasten the process of scrambling somehow by opening new windows)